# -*- coding: utf-8 -*-
"""
GraphVisual
===========
Module providing Graph visuals for rendering graphs.
Note
----
This module is porviding vispy visuals only.
See :mod:`PlotGraph3d` module for plotting.
"""
__author__ = 'Christoph Kirst <ckirst@rockefeller.edu>'
__license__ = 'MIT License <http://www.opensource.org/licenses/mit-license.php>'
__copyright__ = 'Copyright (c) 2017 by Christoph Kirst, The Rockefeller University, New York City'
import numpy as np
import vispy.visuals as visuals
import ClearMap.Analysis.Graphs.GraphRendering as gr
import ClearMap.Visualization.Color as col
###############################################################################
### Graph visuals
###############################################################################
default_color = (0.8, 0.1, 0.1, 1.0);
[docs]class GraphLineVisual(visuals.LineVisual):
"""Displays a graph in 3d using tube rendering for the edges
"""
def __init__(self, graph,
coordinates = None,
color = None, vertex_colors = None, edge_colors = None,
width = None, mode = 'gl'):
connectivity = graph.edge_connectivity();
if coordinates is None:
name = 'coordinates'
else:
name = coordinates;
coordinates = graph.vertex_property(name);
if vertex_colors is not None or edge_colors is not None:
color = None;
if color is None:
if edge_colors is None and vertex_colors is None:
color = default_color;
elif vertex_colors is not None:
if isinstance(vertex_colors, np.ndarray) and vertex_colors.ndim == 2:
color = vertex_colors;
else:
color = col.color(vertex_colors, alpha=True);
elif edge_colors is not None:
if isinstance(edge_colors, np.ndarray) and edge_colors.ndim == 2:
#need a vertex pair for every edge if the color is different
coordinates = coordinates[connectivity.flatten()];
connectivity = np.arange(coordinates.shape[0]);
connectivity = connectivity.reshape((-1,2));
indices = np.arange(len(edge_colors));
indices = np.array([indices, indices]).T.flatten();
color = edge_colors[indices];
else:
color = col.color(edge_colors, alpha=True);
else:
color = col.color(color, alpha=True);
if width is None:
width = 1;
visuals.LineVisual.__init__(self, coordinates, connect=connectivity,
color=color, width=width, method=mode)
[docs]class GraphMeshVisual(visuals.mesh.MeshVisual):
"""Displays a graph in 3d using tube rendering for the edges
"""
def __init__(self, graph,
coordinates = None, radii = None,
n_tube_points = 8, default_radius = 1,
color = None, vertex_colors = None, edge_colors = None,
mode = 'triangles', shading = 'smooth'):
if vertex_colors is not None or edge_colors is not None:
color = None;
if color is None and vertex_colors is None:
color = default_color;
if graph.has_edge_geometry():
if coordinates is None:
name = 'coordinates';
else:
name = coordinates;
coordinates, indices = graph.edge_geometry(name=name, return_indices=True, as_list=False);
#calculate mesh
try:
if radii is None:
name = 'radii';
else:
name = radii;
radii = graph.edge_geometry(name=name, return_indices=False, as_list=False);
except:
print('No radii found in the graph, using uniform radii = %r!' % default_radius);
radii = default_radius * np.ones(coordinates.shape[0]);
else:
coordinates = graph.vertex_coordinates();
indices = graph.edge_connectivity().flatten();
coordinates = np.vstack(coordinates[indices]);
try:
radii = graph.vertex_radii();
radii = radii[indices];
except:
print('No radii found in the graph, using uniform radii = %r!' % default_radius);
radii = default_radius * np.ones(coordinates.shape[0]);
n_edges = graph.n_edges;
indices = np.array([2*np.arange(0,n_edges), 2*np.arange(1,n_edges+1)]).T;
#print(radii.shape, indices.shape, coordinates.shape)
if vertex_colors is not None:
connectivity = graph.edge_connectivity();
edge_colors = (vertex_colors[connectivity[:,0]] + vertex_colors[connectivity[:,1]])/2.0;
vertices, faces, vertex_colors = gr.mesh_tube_from_coordinates_and_radii(coordinates, radii, indices, n_tube_points=n_tube_points, edge_colors=edge_colors, processes=None);
visuals.mesh.MeshVisual.__init__(self, vertices, faces,
color=color, vertex_colors=vertex_colors,
shading=shading, mode=mode)
###############################################################################
### Tests
###############################################################################
def _test():
import numpy as np
import vispy
import ClearMap.Analysis.Graphs.GraphGt as ggt
import ClearMap.Visualization.Vispy.Plot3d as p3d
import ClearMap.Visualization.Vispy.GraphVisual as gv
#reload(gv)
g = ggt.Graph();
g.add_vertex(5);
g.add_edge([[0,1],[1,2],[2,3],[3,4],[4,0]]);
g.set_vertex_coordinates(20*np.random.rand(5,3))
v = vispy.scene.visuals.create_visual_node(gv.GraphLineVisual)
p = v(g, parent=p3d.initialize_view().scene)
p3d.center(p)
v = vispy.scene.visuals.create_visual_node(gv.GraphMeshVisual)
p = v(g, parent=p3d.initialize_view().scene)
p3d.center(p)
Source
